suppressMessages(library(ArchR))
ss <- function(x, pattern, slot = 1, ...) { sapply(strsplit(x = x, split = pattern, ...), '[', slot) }
options(stringsAsFactors = F)
options(repr.plot.width=11, repr.plot.height=8.5)
##################################
### set Arrow File parameters ####
addArchRThreads(threads = 10)
##################################
### load rheMac10 ArchR genome ###
GENOMEDIR='/home/bnphan/resources/genomes/rheMac10'
load(file.path(GENOMEDIR,'rheMac10_liftoff_GRCh38.p13_ArchR_annotations.rda'))
Setting default number of Parallel threads to 10.
PROJDIR='../../../data/raw_data/rheMac10/Stauffer_caudate'
ARCHDIR=file.path(PROJDIR,'ArchR_Stauffer_caudate')
proj = loadArchRProject(ARCHDIR)
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# plot the confusion matrix of cell types by subjects
cM <- confusionMatrix(paste0(proj$ClustersI150), paste0(proj$Sample))
cM <- cM / Matrix::colSums(cM)
p <- pheatmap::pheatmap(
mat = as.matrix(cM),
color = paletteContinuous("whiteBlue"),
border_color = "black")
p
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersI150", embedding = "UMAP")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Sample", embedding = "UMAP")
ggAlignPlots(p1, p2, type = "h")
p1
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a4d2ba731-Date-2021-02-03_Time-11-00-12.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a4d2ba731-Date-2021-02-03_Time-11-00-12.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a59ac0ceb-Date-2021-02-03_Time-11-00-21.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a59ac0ceb-Date-2021-02-03_Time-11-00-21.log
# Broad MSN marker, mouse 2010300C02Rik == human KIAA1211L
# MSN markers, Ppp1r1b = DARPP-32, Bcl11b=Ctip2
markMSN3 = c('Ppp1r1b','Bcl11b','Pde1b','Foxp1','Six3' )
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN3, embedding = "UMAP", imputeWeights = NULL)
p3 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p3))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a7b39123b-Date-2021-02-03_Time-11-00-29.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2021-02-03 11:00:29 : Plotting Embedding 1 2 3 4 5 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a7b39123b-Date-2021-02-03_Time-11-00-29.log
markMSN1 = c('Drd1','Tac1','Foxp2','Slc35d3','Chrm4', 'Pdyn') # D1 markers
# D1 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN1, embedding = "UMAP", imputeWeights = NULL) #
p1 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) +
theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p1))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a4e7dd719-Date-2021-02-03_Time-11-00-40.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2021-02-03 11:00:41 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a4e7dd719-Date-2021-02-03_Time-11-00-40.log
markMSN2 = c('Drd2','Adora2a','Penk', 'Grik3', 'Sp9', 'Gpr52')# D2 markers
# D2 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN2, embedding = "UMAP", imputeWeights = NULL)
p2 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme(axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(nrow = 2),p2))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a2ccad4-Date-2021-02-03_Time-11-00-53.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2021-02-03 11:00:53 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a2ccad4-Date-2021-02-03_Time-11-00-53.log
## plot more interneuron markers
markerGenes1 <- c('Lhx6', "Pvalb", 'Pthlh','Cck','Sst', 'Chat','Th', 'Vip') # Interneuron markers
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", imputeWeights = NULL,
name = markerGenes1, embedding = "UMAP")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(nrow = 2),p))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a4137bde2-Date-2021-02-03_Time-11-01-04.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2021-02-03 11:01:05 : Plotting Embedding 1 2 3 4 5 6 7 8 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a4137bde2-Date-2021-02-03_Time-11-01-04.log
## Neuron vs. Glia markers
markerGenes1 <- c('Drd1', # D1 MSN
'Adora2a', #D2 MSN
'Foxp2', # Striatonigral MSN
'Lhx6', #Interneuron
'Aqp4', # Astrocyte
'Cx3cr1', # Microglia
'Pdgfra', #OPC
'Mog' ,# Oligo,
'Cemip', # mural-fibroblast like
'Itga1' # endothelia
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAP", imputeWeights = NULL)
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(nrow = 2),p))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a173c3716-Date-2021-02-03_Time-11-01-17.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2021-02-03 11:01:17 : Plotting Embedding 1 2 3 4 5 6 7 8 9 10 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a173c3716-Date-2021-02-03_Time-11-01-17.log
## make UMAP plots of
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersI150", embedding = "UMAP")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "DoubletEnrichment", embedding = "UMAP")
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "nFrags", embedding = "UMAP")
ggAlignPlots(p1, p2,p3, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a4ee19100-Date-2021-02-03_Time-11-01-32.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a4ee19100-Date-2021-02-03_Time-11-01-32.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a1f91c319-Date-2021-02-03_Time-11-01-32.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a1f91c319-Date-2021-02-03_Time-11-01-32.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a1fc0867f-Date-2021-02-03_Time-11-01-33.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a1fc0867f-Date-2021-02-03_Time-11-01-33.log
############################################
# using marker gene scores, give cluster names
remapClust <- c(
'C1' = 'MSN_SN',
'C2' = 'Drop', # doublet
'C3' = 'UNK1',
'C4' = 'Drop', # slushbucket MSNs, low frag cells
'C5' = 'MSN_D1',
'C6' = 'MSN_D2',
'C7' = 'MSN_D1',
'C8' = 'MSN_D2',
'C9' = 'Microglia',
'C10'= 'Drop',
'C11'= 'UNK2',
'C12'= 'Oligo',
'C13'= 'Oligo',
'C14'= 'UNK3',
'C15'= 'Astro',
'C16'= 'Drop',
'C17'= 'Astro',
'C18'= 'Drop',
'C19'= 'OPC',
'C20'= 'INT_UNK',
'C21'= 'INT_Pvalb'
)
proj$Clusters2 <- mapLabels(proj$ClustersI150, newLabels = remapClust,
oldLabels = names(remapClust))
table(proj$Clusters2)
proj = saveArchRProject(ArchRProj = proj)
Astro Drop INT_Pvalb INT_UNK Microglia MSN_D1 MSN_D2 MSN_SN
1665 1861 127 221 1028 1635 1763 192
Oligo OPC UNK1 UNK2 UNK3
2901 556 87 31 159
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Clusters2", embedding = "UMAP")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "DoubletEnrichment", embedding = "UMAP")
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "nFrags", embedding = "UMAP")
ggAlignPlots(p1, p2,p3, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a11e1e0e3-Date-2021-02-03_Time-11-01-40.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a11e1e0e3-Date-2021-02-03_Time-11-01-40.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a7b8aa23d-Date-2021-02-03_Time-11-01-41.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a7b8aa23d-Date-2021-02-03_Time-11-01-41.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-40d2a68da0703-Date-2021-02-03_Time-11-01-41.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-40d2a68da0703-Date-2021-02-03_Time-11-01-41.log
# drop the drop clusters
ARCHDIR2=file.path(PROJDIR,'ArchR_Stauffer_caudate_labeled')
idxSample <- BiocGenerics::which(! grepl('Drop|UNK', proj$Clusters2) )
cellsSample <- proj$cellNames[idxSample]
proj2 = subsetArchRProject(
ArchRProj = proj,
cells = cellsSample,
outputDirectory = ARCHDIR2, force = TRUE
)
Dropping ImputeWeights Since You Are Subsetting Cells! ImputeWeights is a cell-x-cell Matrix!
Copying ArchRProject to new outputDirectory : /projects/pfenninggroup/machineLearningForComputationalBiology/snATAC_cross_species_caudate/data/raw_data/rheMac10/Stauffer_caudate/ArchR_Stauffer_caudate_labeled
Copying Arrow Files...
Getting ImputeWeights
No imputeWeights found, returning NULL
Copying Other Files...
Copying Other Files (1 of 2): Embeddings
Copying Other Files (2 of 2): IterativeLSI
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# make group coverage, call peaks, and
proj2<-addGroupCoverages(proj2, groupBy="Clusters2", force = TRUE)
proj2 = saveArchRProject(ArchRProj = proj2)
ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-40d2a57ecb21d-Date-2021-02-03_Time-11-09-22.log
If there is an issue, please report to github with logFile!
Astro (1 of 8) : CellGroups N = 2
INT_Pvalb (2 of 8) : CellGroups N = 2
Microglia (3 of 8) : CellGroups N = 2
MSN_D1 (4 of 8) : CellGroups N = 2
MSN_D2 (5 of 8) : CellGroups N = 2
MSN_SN (6 of 8) : CellGroups N = 2
Oligo (7 of 8) : CellGroups N = 2
OPC (8 of 8) : CellGroups N = 2
2021-02-03 11:09:23 : Further Sampled 4 Groups above the Max Fragments!, 0.02 mins elapsed.
2021-02-03 11:09:24 : Creating Coverage Files!, 0.026 mins elapsed.
2021-02-03 11:09:24 : Batch Execution w/ safelapply!, 0.026 mins elapsed.
2021-02-03 11:15:53 : Adding Kmer Bias to Coverage Files!, 6.513 mins elapsed.
Completed Kmer Bias Calculation
Adding Kmer Bias (1 of 16)
Adding Kmer Bias (2 of 16)
Adding Kmer Bias (3 of 16)
Adding Kmer Bias (4 of 16)
Adding Kmer Bias (5 of 16)
Adding Kmer Bias (6 of 16)
Adding Kmer Bias (7 of 16)
Adding Kmer Bias (8 of 16)
Adding Kmer Bias (9 of 16)
Adding Kmer Bias (10 of 16)
Adding Kmer Bias (11 of 16)
Adding Kmer Bias (12 of 16)
Adding Kmer Bias (13 of 16)
Adding Kmer Bias (14 of 16)
Adding Kmer Bias (15 of 16)
Adding Kmer Bias (16 of 16)
2021-02-03 11:23:30 : Finished Creation of Coverage Files!, 14.127 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-addGroupCoverages-40d2a57ecb21d-Date-2021-02-03_Time-11-09-22.log
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# call peaks
proj2<-addReproduciblePeakSet(proj2, groupBy = "Clusters2", plot = FALSE, genomeSize = 2.7e9)
proj2 = saveArchRProject(ArchRProj = proj2)
Searching For MACS2.. Found with $path! ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-40d2a21ad04e-Date-2021-02-03_Time-11-23-34.log If there is an issue, please report to github with logFile! Calling Peaks with Macs2 2021-02-03 11:23:34 : Peak Calling Parameters!, 0.004 mins elapsed.
Group nCells nCellsUsed nReplicates nMin nMax maxPeaks Astro Astro 1665 1000 2 500 500 150000 INT_Pvalb INT_Pvalb 127 127 2 53 74 63500 Microglia Microglia 1028 997 2 497 500 150000 MSN_D1 MSN_D1 1635 1000 2 500 500 150000 MSN_D2 MSN_D2 1763 1000 2 500 500 150000 MSN_SN MSN_SN 192 192 2 92 100 96000 Oligo Oligo 2901 1000 2 500 500 150000 OPC OPC 556 556 2 256 300 150000
2021-02-03 11:23:34 : Batching Peak Calls!, 0.004 mins elapsed.
2021-02-03 11:23:35 : Batch Execution w/ safelapply!, 0 mins elapsed.
2021-02-03 12:16:57 : Identifying Reproducible Peaks!, 53.372 mins elapsed.
2021-02-03 12:18:06 : Creating Union Peak Set!, 54.528 mins elapsed.
Converged after 6 iterations!
2021-02-03 12:18:14 : Finished Creating Union Peak Set (391927)!, 54.666 mins elapsed.
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# add peak counts matrix
proj2 <- addPeakMatrix(proj2)
proj2 = saveArchRProject(ArchRProj = proj2)
ArchR logging to : ArchRLogs/ArchR-addPeakMatrix-40d2a7d59c1d3-Date-2021-02-03_Time-12-18-21.log
If there is an issue, please report to github with logFile!
2021-02-03 12:18:22 : Batch Execution w/ safelapply!, 0 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-addPeakMatrix-40d2a7d59c1d3-Date-2021-02-03_Time-12-18-21.log
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# add motif enrichment matrix
proj2 <- addMotifAnnotations(ArchRProj = proj2, motifSet = "JASPAR2018", name = "Motif")
proj2 = saveArchRProject(ArchRProj = proj2)
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘TFBSTools’
ArchR logging to : ArchRLogs/ArchR-addMotifAnnotations-40d2a7b4babdd-Date-2021-02-03_Time-12-22-44.log
If there is an issue, please report to github with logFile!
2021-02-03 12:22:45 : Gettting Motif Set, Species : , 0.002 mins elapsed.
2021-02-03 12:23:11 : Finding Motif Positions with motifmatchr!, 0.436 mins elapsed.
2021-02-03 12:35:53 : Creating Motif Overlap Matrix, 13.129 mins elapsed.
2021-02-03 12:36:05 : Finished Getting Motif Info!, 13.328 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-addMotifAnnotations-40d2a7b4babdd-Date-2021-02-03_Time-12-22-44.log
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# add motif deviations matrix
proj2 <- addBgdPeaks(proj2)
proj2 <- addDeviationsMatrix(proj2, peakAnnotation = "Motif", force = TRUE)
proj2 = saveArchRProject(ArchRProj = proj2)
Identifying Background Peaks! Using Previous Background Peaks! ArchR logging to : ArchRLogs/ArchR-addDeviationsMatrix-40d2a3b2cb4ae-Date-2021-02-03_Time-12-36-45.log If there is an issue, please report to github with logFile!
NULL
2021-02-03 12:36:51 : Batch Execution w/ safelapply!, 0 mins elapsed.
###########
2021-02-03 15:49:54 : Completed Computing Deviations!, 193.152 mins elapsed.
###########
ArchR logging successful to : ArchRLogs/ArchR-addDeviationsMatrix-40d2a3b2cb4ae-Date-2021-02-03_Time-12-36-45.log
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# add co-accessibility matrix
proj2 <- addCoAccessibility(proj2, reducedDims = "HarmonyI150", dimsToUse = 1:30,
scaleDims = TRUE, corCutOff = 0.75, k = 100,
knnIteration = 500, overlapCutoff = 0.8,
maxDist = 1e+05, scaleTo = 10^4, log2Norm = TRUE)
proj2 = saveArchRProject(ArchRProj = proj2)
ArchR logging to : ArchRLogs/ArchR-addCoAccessibility-40d2a26e6efcf-Date-2021-02-03_Time-15-50-03.log
If there is an issue, please report to github with logFile!
2021-02-03 15:50:03 : Computing KNN, 0.004 mins elapsed.
2021-02-03 15:50:03 : Identifying Non-Overlapping KNN pairs, 0.005 mins elapsed.
2021-02-03 15:50:06 : Identified 480 Groupings!, 0.048 mins elapsed.
2021-02-03 15:50:12 : Computing Co-Accessibility chr1 (1 of 21), 0.151 mins elapsed.
2021-02-03 15:50:36 : Computing Co-Accessibility chr2 (2 of 21), 0.559 mins elapsed.
2021-02-03 15:50:52 : Computing Co-Accessibility chr3 (3 of 21), 0.826 mins elapsed.
2021-02-03 15:51:08 : Computing Co-Accessibility chr4 (4 of 21), 1.088 mins elapsed.
2021-02-03 15:51:23 : Computing Co-Accessibility chr5 (5 of 21), 1.34 mins elapsed.
2021-02-03 15:51:34 : Computing Co-Accessibility chr6 (6 of 21), 1.524 mins elapsed.
2021-02-03 15:51:49 : Computing Co-Accessibility chr7 (7 of 21), 1.762 mins elapsed.
2021-02-03 15:52:06 : Computing Co-Accessibility chr8 (8 of 21), 2.061 mins elapsed.
2021-02-03 15:52:19 : Computing Co-Accessibility chr9 (9 of 21), 2.263 mins elapsed.
2021-02-03 15:52:31 : Computing Co-Accessibility chr10 (10 of 21), 2.471 mins elapsed.
2021-02-03 15:52:44 : Computing Co-Accessibility chr11 (11 of 21), 2.685 mins elapsed.
2021-02-03 15:52:57 : Computing Co-Accessibility chr12 (12 of 21), 2.899 mins elapsed.
2021-02-03 15:53:07 : Computing Co-Accessibility chr13 (13 of 21), 3.075 mins elapsed.
2021-02-03 15:53:18 : Computing Co-Accessibility chr14 (14 of 21), 3.255 mins elapsed.
2021-02-03 15:53:33 : Computing Co-Accessibility chr15 (15 of 21), 3.504 mins elapsed.
2021-02-03 15:53:44 : Computing Co-Accessibility chr16 (16 of 21), 3.684 mins elapsed.
2021-02-03 15:53:56 : Computing Co-Accessibility chr17 (17 of 21), 3.894 mins elapsed.
2021-02-03 15:54:05 : Computing Co-Accessibility chr18 (18 of 21), 4.031 mins elapsed.
2021-02-03 15:54:11 : Computing Co-Accessibility chr19 (19 of 21), 4.145 mins elapsed.
2021-02-03 15:54:22 : Computing Co-Accessibility chr20 (20 of 21), 4.317 mins elapsed.
2021-02-03 15:54:33 : Computing Co-Accessibility chrX (21 of 21), 4.502 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-addCoAccessibility-40d2a26e6efcf-Date-2021-02-03_Time-15-50-03.log
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|